Secondary structure assignment for conformationally irregular peptides: Comparison between DSSP, STRIDE and KAKSI

Zhang, Y.; Sagui, Celeste

doi:10.1016/j.jmgm.2014.10.005

Cited by 45 publications

(43 citation statements)

References 94 publications

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“…2005;Martin et al 2005;Oluwatobi Salawu 2016;Parisien and Major 2005;Park et al 2011;Richards and Kundrot 1988;Sklenar et al 1989;Zacharias and Knapp 2014). They have been defined with various criteria (Offmann et al 2007): the most popular SSAM use backbone hydrogen bonding pattern-based methods (Carter et al 2003;Fodje and Al-Karadaghi 2002;Frishman and Argos 1995;Kabsch and Sander 1983;Zhang and Sagui 2015).…”

Section: Developments In Ppii Structural Assignmentmentioning

confidence: 99%

Recent advances on polyproline II

et al. 2017

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About half of the globular proteins are composed of regular secondary structures, α-helices, and β-sheets, while the rest are constituted of irregular secondary structures, such as turns or coil conformations. Other regular secondary structures are often ignored, despite their importance in biological processes. Among such structures, the polyproline II helix (PPII) has interesting behaviours. PPIIs are not usually associated with conventional stabilizing interactions, and recent studies have observed that PPIIs are more frequent than anticipated. In addition, it is suggested that they may have an important functional role, particularly in protein-protein or protein-nucleic acid interactions and recognition. Residues associated with PPII conformations represent nearly 5% of the total residues, but the lack of PPII assignment approaches prevents their systematic analysis. This short review will present current knowledge and recent research in PPII area. In a first step, the different methodologies able to assign PPII are presented. In the second step, recent studies that have shown new perspectives in PPII analysis in terms of structure and function are underlined with three cases: (1) PPII in protein structures. For instance, the first crystal structure of an oligoproline adopting an all-trans polyproline II (PPII) helix had been presented; (2) the involvement of PPII in different diseases and drug designs; and (3) an interesting extension of PPII study in the protein dynamics. For instance, PPIIs are often linked to disorder region analysis and the precise analysis of a potential PPII helix in hypogonadism shows unanticipated PPII formations in the patient mutation, while it is not observed in the wild-type form of KISSR1 protein.

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Section: Developments In Ppii Structural Assignmentmentioning

confidence: 99%

Recent advances on polyproline II

et al. 2017

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“…Although DSSP and STRIDE demonstrate excellent agreement for ordered peptide/protein structures, there may be significant differences when they are utilized for the analysis of inherently disordered peptides. 112 Due to the difficulty in accurately assigning a compensatory factor to accommodate these differences, we assumed that the two results were approximately equal for our analysis. Our previously published results with CHARMM36 force field 26 show a higher propensity to sample the -sheet region of conformational space, which is still outside of statically significant similarity when compared to CD, but it confirms the AFM dynamic force spectroscopy results that both A(1-40) and its residues 13−23 fragment form stable dimers in most likely antiparallel manner.…”

Section: Discussionmentioning

confidence: 99%

“…The separation between highest and lowest energy groups were: 5.0 kJ•mol -1 , 5.7 kJ•mol -1 , 4.6 kJ•mol -1 , and 4.1 kJ•mol -1 , respectively, AMBER-ILDN, AMBER-ILDN*, AMBER-NMR, and CHARMM22* with a previously published value of 4.1 kJ•mol -1 for CHARMM36 26. Secondary structure analysis was performed using the DSSP method (structures in the figure may have small differences since YASARA uses the STRIDE algorithm) 112. The lowest energy representative structure for AMBER-ILDN force field had a dimerSASA of 72.31 nm 2 with an ISA of 10.10 nm 2 .…”

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confidence: 99%

Effects of Force Fields on the Conformational and Dynamic Properties of Amyloid β(1-40) Dimer Explored by Replica Exchange Molecular Dynamics Simulations

Watts

Gregory

Frisbie

et al. 2017

Preprint

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Alzheimer's disease is histologically marked by fibrils of Amyloid beta (A) peptide within the extracellular matrix. Fibrils themselves are benign compared to the cytotoxicity of the oligomers and pre-fibrillary aggregates. The conformational space and structural ensembles of A peptides and their oligomers in solution are inherently disordered and proven to be challenging to study.Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the A(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using:

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“…On the basis of the above datasets, we extract effective protein features as experimental data by using DSSP [5] software to generate the dssp file of each protein strand. And then extract the sequence information and corresponding secondary structure information of the protein sequences from their dssp file.…”

Section: Datasetmentioning

confidence: 99%

A Protein Secondary Structure Prediction Method Based on BP Neural Network

Yin¹,

Liu²,

Wei³

et al. 2017

dtcse

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Abstract. Protein structure prediction is a main task in the field of bioinformatics, and the prediction of protein secondary structure is the key point of this task. Extracting representative features and efficient classification methods are the basis of the prediction process. In this paper, a prediction method based on BP neural network is proposed. We use valid protein features extracted by variable-sized sliding window and two different encoding modes (5-bit encoding and Profile encoding) as input data, to make predictions for the secondary structure of proteins. The prediction accuracies are calculated by Jackknife test on three commonly used low-similarity protein datasets: 25PDB, 1189 and 640, and this method achieves a high overall accuracy upon these three datasets.

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Secondary structure assignment for conformationally irregular peptides: Comparison between DSSP, STRIDE and KAKSI

Cited by 45 publications

References 94 publications

Recent advances on polyproline II

Recent advances on polyproline II

Effects of Force Fields on the Conformational and Dynamic Properties of Amyloid β(1-40) Dimer Explored by Replica Exchange Molecular Dynamics Simulations

A Protein Secondary Structure Prediction Method Based on BP Neural Network

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